Zinc in PDB 6uij: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate, PDB code: 6uij was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.83 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.780, 80.780, 242.602, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.9

Other elements in 6uij:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate (pdb code 6uij). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate, PDB code: 6uij:

Zinc binding site 1 out of 1 in 6uij

Go back to Zinc Binding Sites List in 6uij
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:57.4
occ:1.00
OD2 A:ASP174 1.9 47.8 1.0
OD2 A:ASP267 2.0 52.5 1.0
S11 A:SS9701 2.2 54.4 1.0
ND1 A:HIS176 2.3 57.8 1.0
CG A:ASP174 2.7 48.6 1.0
OD1 A:ASP174 2.8 55.9 1.0
CG A:ASP267 3.1 54.7 1.0
CE1 A:HIS176 3.1 57.3 1.0
CG A:HIS176 3.3 49.0 1.0
C9 A:SS9701 3.4 53.5 1.0
OD1 A:ASP267 3.4 55.2 1.0
C10 A:SS9701 3.5 54.7 1.0
CB A:HIS176 3.7 49.6 1.0
N A:HIS176 3.9 49.9 1.0
CB A:ASP174 4.1 50.7 1.0
NE2 A:HIS136 4.2 51.0 1.0
NE2 A:HIS176 4.2 59.0 1.0
N A:VAL175 4.3 54.6 1.0
CE1 A:HIS136 4.3 49.2 1.0
CA A:GLY305 4.3 53.1 1.0
CD2 A:HIS176 4.3 53.1 1.0
CB A:ASP267 4.4 56.5 1.0
CA A:HIS176 4.4 46.8 1.0
CE2 A:TYR307 4.4 57.4 1.0
CG1 A:VAL175 4.5 52.7 1.0
NE2 A:HIS137 4.5 51.4 1.0
OH A:TYR307 4.6 58.8 1.0
N A:GLY305 4.6 58.3 1.0
C A:VAL175 4.8 53.3 1.0
C8 A:SS9701 4.8 52.1 1.0
CA A:ASP174 4.9 48.6 1.0
C A:ASP174 4.9 55.0 1.0
CA A:VAL175 5.0 51.1 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906
Page generated: Wed Dec 16 12:59:14 2020

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